"No faction is a monolith, and player decisions affect which sub-faction will be ascendant. When working with Theleme, players can side with the Inquisitors, who take a hardline convert-or-die approach to the natives, or with the Missionaries, who believe that they will eventually win converts to their faith by living peacefully with the locals. Some native clans believe that they can profit from the riches and weapons the settlers brought with them, while others want to drive them back into the sea."
So I guess it's our choice if Theleme will be outright evil